Some tips on HDF5 files

In general, my users ask me to export HDF formatted images into something directly usable with GIS desktop software (Geotiff, Erdas Imagine, etc.)

The problem with HDF is that it is not an image format but a data container format: it’s very general, can contain any type of object (variables, arrays, images…). The best way to handle this format is to write some lines of code to browse the file internal table storing the meta information.

From the command line, you can use gdalinfo to get some meta-information. The meta information can be more or less complex depending on what was stored in the HDF file.
Let’s consider an HDF5 file, which metainformation would be

Driver: HDF5/Hierarchical Data Format Release 5
Size is 512, 512
Coordinate System is `'
SUBDATASET_0_DESC=[1511x701] //FVC (8-bit integer)
SUBDATASET_1_DESC=[1511x701] //FVC_QF (8-bit character)
SUBDATASET_2_DESC=[1511x701] //FVC_err (8-bit integer)
Corner Coordinates:
Upper Left ( 0.0, 0.0)
Lower Left ( 0.0, 512.0)
Upper Right ( 512.0, 0.0)
Lower Right ( 512.0, 512.0)
Center ( 256.0, 256.0)

In HDF you can store different types of data in the same file, the Size information for the file is not meaningful in this case (here it is written that Size is 512, 512, which is wrong since the actual size of the images is given on the lines with the SUBADATASET_0_DESC.

The image size given in the header is not meaninful: the images are 1511×701 lines, as indicated in the line SUBDATASET_0_DESC and not 512×512 in the header. The same SUBADATASET_0_DESC line gives you the file type.

The example above is about an HDF5 image, but FWTools can also handle HDF4 images.

Now, to export the image to something easier to handle, you must give the dataset name to gdal_translate, not the hdf5 file name:

gdal_translate -of gtiff HDF5:"HDF5_LSASAF_MSG_FVC_SAme_200806100000"://FVC fvc.tif

to export the data set named FVC into a single image.


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